A different way of looking at the Lord's world

Why ID part 4

The difference between LIVING and non-living is DNA and all of its many components. We will try to give a brief, but detailed study of this particular chemical and try to understand what the DNA enigma is. How DNA was discovered has been the subject of many fascinating books- I suggest the first 5 chapters of “Signature in the Cell” by Stephen Meyers for a good history.

DNA is made up of 4 distinct chemicals (adenine [A], thymine [T], cytosine [C] and guanine [G] that provide the information of life (not really, as in all things there are exceptions to the rule sometimes, thymine [T]is replaced with uracil [U]).

Notice they form two groups: 1) pyrimidines: a nitrogenous base with a six-sided ring structure; a biologically significant derivative of pyrimidine, especially the bases cytosine, thymine, and uracil found in RNA and DNA and 2) purines: a nitrogen-containing substance derived from uric acid that is the precursor of several biologically important compounds; a derivative of purine, especially either of the bases adenine and guanine, which are found in RNA and DNA. Bio-chemists knew that the same amount of Thymine and Adenine as well as the same amount of Cytosine and Guanine existed in each chromosome.

We knew that there is a structural asymmetry in the construction of the backbone of the DNA molecule. The phosphate groups attach to a different carbon molecule on one side of the ribose sugar than they do on the other. On one side of the ring structure of the sugar, the phosphate attaches to what is called its 5′ carbon (five prime carbon); on the other, the phosphate attaches to what is called its 3′ carbon. It was known by chemists for a long time but nobody had the insight to understand the nature of the double helix. Everyone was trying to make the two backbone run parallel to each other.

This did not work- all kinds of odd ball models were being developed and published and then rejected by bio-chemists. Then along came the contrarians Watson and Crick. Crick realized that the pattern she was describing— called a “monoclinic C2 symmetry” pattern— was indicative of an anti-parallel double helix structure. Instead of the two strands running from 5′ to 3′ in the same direction, Crick realized that Franklin’s data indicated that one helix was running up in the 5′ to 3′ direction and the other strand was running down in the 5′ to 3′ direction the other way. Watson as he was building the model realized that they were two separate strands entwined around each other.

The Watson-Crick model clearly indicated that DNA had an impressive chemical and structural complexity. It was a very long molecule composed on the outside by a regular arrangement of sugar and phosphate molecules. On the inside, it could contain an almost infinite variety of different arrangements of the four bases. This produced an impressive potential for variability and complexity of sequence as required by any potential carrier of hereditary information. Most biologists thought life consisted solely of matter and energy. However, after Watson and Crick, biologists came to recognize the importance of a third fundamental entity in living things: information. At some point in the history of the universe, biological information came into existence. Nevertheless, how?

Theories that claim to explain the origin of the first life must answer this question. How could disparate chemicals bond together in such a manner as to pass on information to a receptor that could read it? How did the receptor develop? What we are talking about here is ‘biological/chemical information’ and the beginning of LIFE itself.

What is ‘biological information’? Both philosophers and biologists have contributed to an ongoing foundational discussion of the status of this mode of description in biology. It is generally agreed that the sense of information isolated by Claude Shannon and used in mathematical information theory is legitimate, useful, and relevant in many parts of biology. In this sense, anything is a source of information if it has a range of possible states, and one variable carries information about another to the extent that their states are physically correlated. We will cover Shannon’s law in more detail later.

Details about this image will become available as we continue on the path of the mystery of the mystery. In Darwin’s time few, if any, biologists talked about biological or genetic information (that information just was not known at the time), but today they routinely refer to DNA, RNA, mRNA, tRNA and proteins as carriers or repositories of information. Biologists will tell us that DNA stores and transmits “genetic information (without really knowing what ‘that’ is), that it expresses a “genetic message (they can see what that is),” that it stores “assembly instructions (they can see what is created) ,” a “genetic blueprint,” or “digital code.” Biology has entered its own information age, and scientists seeking to explain the origin of life have taken note. Life does not consist of just matter and energy, but also information. According to evolutionists, matter and energy were around long before life, so this third aspect of living systems has now taken center stage. At some point in the history of the universe, biological information came into existence. But how? Theories that claim to explain the origin of the first life must answer this question. However, what exactly is information? What is biological information? Beginning in the late 1940s, mathematicians and computer scientists began to define, study, measure, and quantify information. However, they made distinctions between several distinct types or conceptions of information. What kind of information does DNA have? What kind of information must origin-of-life researchers “explain the origin of”? It is important to answer these questions because DNA contains a particular kind of information, one that only deepens the mystery surrounding its origin.

If you did not read the above link, good luck on understanding the following. We left that document with the question: So what kind of information does DNA possess, Shannon information or some other?

We need to look at what molecular biologists have discovered since 1953 about the role of DNA within the miniature world of the cell. In the wake of Watson and Crick’s seminal 1953 paper, scientists soon realized that DNA could store an immense amount of information. The chemistry of the molecule allows any one of the four (or five if discussing RNA) bases to attach to any of the sugar molecules in the backbone. This allows the kind of almost incalculable variable sequencing that any carrier of genetic information would need to have. In addition, the weak hydrogen bonds that hold the two anti-parallel strands together suggest a way the molecule might allow itself to be unzipped. This allows the exposed sequence of bases to be duplicated in a unique and fascinating manner. It would seem that DNA was ideal for storing information-rich sequences of chemical (alphabetic) characters.

However, how DNA expressed this information and how it could possibly be using that information remained uncertain. These answers would come due to new developments in the field of protein chemistry. Scientists today know that protein molecules perform virtually all of the critical functions in the cell. Proteins build cellular machines and structures, they carry and deliver cellular materials, and they catalyze chemical reactions that the cell needs to stay alive. Proteins also process the genetic information.

To accomplish this critical work, a typical cell uses thousands of different kinds of proteins; each with a distinctive shape related to its function. It is kind of like Microsoft Office.® Access, Excel, PowerPoint, Outlook, Word- all completely different programs, different sizes, different functions, however, they can interact with each other, pass data to and from each other and many other functions that assist you in maintaining top functionality while working on your computer.

By the 1890s, various biochemists had begun to recognize how proteins were central to the maintenance of life in the cells. The biochemists knew proteins were heavy (“ high molecular weight”) molecules that were involved in many of the chemical reactions going on inside cells. Chemists were also able to determine that proteins were made of smaller molecules called amino acids during the first half of the twentieth century. Many scientists, for awhile, thought that proteins were so important that they (the proteins), rather than DNA molecules, were the repositories of genetic information.

Until the 1950s, scientists repeatedly underestimated the complexity of proteins. William Astbury[1] was an outstanding scientist who had studied physics at Cambridge during and after World War I. He then worked with William Bragg[2], the pioneering X-ray crystallographer whose son Lawrence later supervised Watson and Crick. Astbury was convinced that proteins held the key to understanding life. He thought they should exhibit a simple, regular structure that could be described by a mathematical equation or some general law.

He was used to studying highly regular and orderly structures as a crystallographer. Salt crystals, the first structures determined using X-ray techniques, have a highly repetitive or regular structure of sodium and chlorine atoms arranged in a three-dimensional grid, a pattern in which one type of atom always has six of the other types surrounding it.

Astbury was convinced that proteins— the secret of life—life— should exhibit a similar regularity. During the 1930s he made a discovery that seemed to confirm his expectation. Astbury used X rays to determine the molecular structure of a fibrous protein called keratin, the key structural protein in hair and skin.[3] Astbury discovered that keratin exhibits a simple, repetitive molecular structure, with the same pattern of amino acids repeating over and over again— just like the repeating chemical elements in a crystal (or the repeating pattern of bases that P. A. Levene[4] had mistakenly proposed as a structure for DNA). Astbury concluded (unfortunately) that all proteins, including the mysterious globular proteins so important to life, would exhibit the same basic pattern he discovered in keratin. Many of Astbury’s contemporaries shared the same view. In 1937, for example, two leading American biochemists, Max Bergmann[5] and Carl Niemann[6], of the Rockefeller Institute, argued that the amino acids in all proteins occurred in regular, mathematically expressible proportions.[7] It took 25 years before this mistaken thought process was understood and corrected.

About the same time that Watson and Crick were trying to solve the structure of DNA (the late 1950’s), another Cambridge scientist made a discovery that would challenge Astbury’s view of proteins. While working just a couple miles from Watson and Crick at famous Laboratory for Molecular Biology (or LMB), biochemist Fred Sanger[8] determined the structure of the protein molecule insulin. Sanger’s discovery would later earn him the first of two Nobel prizes in chemistry. Sanger showed that insulin consisted of irregular sequences of various amino acids, rather like a string of differently colored beads arranged with no discernible or repeating pattern[9].

The above was the part of chemistry class (both high school and college) that I hated the most-drawing stupid diagrams. To me as long as you knew the formula (C257H383N65O77S6), what the heck difference did it make if you knew the diagram? But some of those old fuddy-duddy’s insisted on you drawing it out exactly like what they had in the book, but it really did not matter when they found out the actual protein looked like below. All that time, energy, arguments and grade points wasted.

Subsequent work on other proteins would show the same thing: the sequencing of amino acids is usually highly irregular and defies description by any general rule.[10]

Many biologists at the time still expected proteins, considered by many the fundamental unit of life, to exhibit regularity, if not in the arrangement of their amino acids, then at least in their overall three-dimensional shapes or structures would end up exhibiting some sort of geometric regularity. Some imagined that insulin and hemoglobin proteins, for example, would look like “bundles of parallel rods[11].” As Johns Hopkins biophysicist George Rose recounts, “Protein structure was a scientific terra incognita[12]. With scant evidence to go on, biologists pictured proteins vaguely as featureless ellipsoids: spheres, cigars, Kaiser rolls[13].”

Then came the publication of a paper by John Kendrew who studied chemistry at Cambridge and graduated in 1939. After doing research on radar technology during the war, he took up the study of molecular biology at the Medical Research Council Laboratory in Cambridge in 1946. There Kendrew began to work closely with Max Perutz, the Austrian crystallographer who, along with Lawrence Bragg, had officially supervised Watson and Crick. In 1958, Kendrew made his own contribution to the molecular biological revolution when he published a paper on the three-dimensional structure of the protein myoglobin[14].

Kendrew’s work revealed an extraordinarily complex and irregular three-dimensional shape, a twisting, turning, tangled chain of amino acids. Whereas protein scientists had anticipated that proteins would manifest the kind of regular order present in crystals, they found instead a complex three-dimensional structure.

In the Nature paper, he wrote, “Perhaps the most remarkable features of the molecule are its complexity and its lack of symmetry. The arrangement seems to be almost totally lacking in the kind of regularities which one instinctively anticipates, and it is more complicated than has been predicted by any theory of protein structure[15].”

Biochemists recognized that proteins exhibited another rather remarkable property. In addition to their complex shapes and irregular arrangements of amino acids, proteins also exhibit ‘specificity’. By specificity, biologists mean that a molecule has some features that have to be what they are, within very fine tolerances, for the molecule to perform an important function in that cell. Any deviation will cause that protein to fail to perform is function.

Proteins show specificity in two ways. First, proteins display a specificity of shape. The strangely irregular shapes of proteins that Kendrew and others discovered are essential to the function of the proteins. In particular, the three-dimensional shape of a protein gives it a close association with other equally specified and complex molecules or with simpler substrates. This enables it to catalyze specific chemical reactions or to build specific structures within the cell. In other words, the proteins all fit together in a certain way, which allows the chemical relationship to proceed.

Because of its three-dimensional specificity, one protein usually cannot substitute for another. A topoisomerase[16] can no more perform the job of a polymerase[17] than Excel can format a letter better than Word.

Enzymes are proteins that catalyze specific chemical reactions. The simplified figure below shows an enzyme called a beta-galactosidase and a two-part sugar molecule (a disaccharide) called lactose. The enzyme’s shape and dimensions must exactly conform to the shape and dimensions of the disaccharide molecule, so that the lactose molecule can nestle into the pockets of the enzyme. Once it does, a chemically active part of the enzyme, called an active site, starts a chemical reaction. The reaction breaks the chemical bonds holding the two parts of the sugar together and liberates two individual molecules of glucose, both of which the cell can use easily.

These two molecules can then be used in further reactions necessary in maintaining the life and health of the cell.

Consider how another example of the specific shape of proteins allows them to perform specific functions. The eukaryotic cell has an uncanny way of storing the information in DNA in a highly compact way (Eukaryotes are cells that contain a nucleus and other membrane-bound organelles; prokaryotic cells lack these features.)

Strands of DNA are wrapped around spool-like structures called nucleosomes. The nucleosomes are made of proteins called histones. It is the specific shape of the histone proteins that enables them to do their job.

Histones 3 and 4, for example, fold into well-defined three-dimensional shapes with a precise distribution of positive electrical charges around their exteriors. This precise shape and charge distribution enables DNA strands to coil efficiently around the nucleosome spools and store an immense amount of information in a very small space[18]. Due to the nucleosome spooling, the information storage density of DNA is many times that of our most advanced silicon chips[19][20].

In the case of nucleosomes, there is an uncanny distribution of positively charged regions on the surface of the histone proteins that exactly matches the negatively charged regions of the double-stranded DNA that coils around it[21].

Proteins have a second type of specificity— one that will explain the first. Proteins do not just display a specificity of shape; they also display a specificity of arrangement. Whereas proteins are built from rather simple amino-acid “building blocks,” their various functions crucially depend on the specific arrangement of those building blocks. The specific sequence of amino acids in a chain and the resulting chemical interactions between amino acids largely determine the specific three-dimensional structure that the chain will adopt when completed. Those structures or shapes determine what function, if any, the amino acid chain can perform in the cell— whether as an enzyme, structural component, or a machine for processing information[22]. Below is a simplified picture of how that might work.

Next up the I will try to tie this all together with the importance of the Sequence Hypothesis, the ‘genetic code’ and the “Shannon Information Plus”. After that the “Origin Of”.

[1] An English physicist and molecular biologist who made pioneering X-ray diffraction studies of biological molecules.

[2] A British physicist and X-ray crystallographer, discoverer (1912) of Bragg’s law of X-ray diffraction, which is basic for the determination of crystal structure

[3] Astbury and Street, “X-Ray Studies of the Structure of Hair, Wool and Related Fibres”; Judson, The Eighth Day of Creation, 61– 62; Olby, The Path to the Double Helix, 63.

[4] An American biochemist who studied the structure and function of nucleic acids. He characterized the different forms of nucleic acid, DNA from RNA, and found that DNA contained adenine, guanine, thymine, cytosine, deoxyribose, and a phosphate group. He specialized in decoding protein and peptide structures.

[5] He developed the Bergmann-Zervas carbobenzoxy method for the synthesis of polypeptides.

[6] an American biochemist who worked extensively on the chemistry and structure of proteins,

[8] In 1958, he was awarded a Nobel Prize in chemistry “for his work on the structure of proteins, especially that of insulin”.

[9] According to Judson: “The man who released the present-day understanding of molecular specificity in living processes was Frederick Sanger. His determination, beginning in the mid-forties, of the amino-acid sequences of bovine insulin proved that they have no general periodicities. His methods and this surprising result had many consequences, of course: the most general and profound was that proteins are entirely and uniquely specified” (The Eighth Day of Creation, 88– 89, 585). See Sanger and Thompson, “The Amino Acid Sequence in the Glycyl Chain of Insulin.”

[14] is an iron- and oxygen-binding protein found in the muscle tissue in almost all mammals. It is related to hemoglobin, which is the iron- and oxygen-binding protein in blood, specifically in the red blood cells.